|
spaces_line = Opt(Spaces())+ AnyEol()
|
|
blast_filter = Str("BLASTN", "BLASTP", "BLASTX", "TBLASTX", "T...
|
|
ncbi_version = Std.application_version(Group("appversion", Re(...
|
|
blastn_appheader = Std.application_name(Str("BLASTN"), {"app":...
|
|
blastp_appheader = Std.application_name(Str("BLASTP"), {"app":...
|
|
blastx_appheader = Std.application_name(Str("BLASTX"), {"app":...
|
|
tblastn_appheader = Std.application_name(Str("TBLASTN"), {"app...
|
|
tblastx_appheader = Std.application_name(Str("TBLASTX"), {"app...
|
|
query_letters = Spaces()+ Str("(")+ Std.query_size(Digits())+ ...
|
|
query_descr = Std.query_description_block(query_descr)
|
|
_comma_digits = Re(r"\d(\d\d?)?(,\d\d\d)+")
|
|
query_database = Str("Database:")+ Opt(Spaces())+ Std.database...
|
|
to_table = Group("to_table", (SkipLinesUntil(Str("Sequences pr...
|
|
table_entry = Std.search_table_entry(Group("table_entry", (Ass...
|
|
table = Std.search_table(Rep(table_entry))
|
|
header = Std.search_header(SkipLinesUntil(Str("Query="))+ quer...
|
|
hit_length = Spaces()+ Str("Length = ")+ Std.hit_length(Digits...
|
|
hit_descr = Str(">")+ Std.hit_description(UntilEol())+ AnyEol(...
|
|
num_bits = Std.hsp_value(Float(), {"name": "bits", "bioformat:...
|
|
expect = Std.hsp_value(Float(), {"name": "expect", "bioformat:...
|
|
num_identical = Std.hsp_value(Digits(), {"name": "identical", ...
|
|
hsp_length = Std.hsp_value(Digits(), {"name": "length", "biofo...
|
|
num_positives = Std.hsp_value(Digits(), {"name": "positives", ...
|
|
score = Re(r" *Score = *")+ num_bits+ Re(r" bits \((?P<XXX1>\d...
|
|
tblastn_score = Re(r" *Score = *")+ num_bits+ Re(r" bits \((?P...
|
|
blastn_identical = Re(r" *Identities = *")+ num_identical+ Str...
|
|
blastp_identical = Re(r" *Identities = *")+ num_identical+ Str...
|
|
frame = Str(" Frame = ")+ Std.hsp_frame(UntilEol(), {"which": ...
|
|
tblastx_frame = Str(" Frame = ")+ Std.hsp_frame(UntilSep(sep= ...
|
|
strand = Re(r" *Strand = ")+(Std.hsp_strand(Str("Plus"), {"str...
|
|
query_line = Std.hsp_seqalign_query_leader(Std.hsp_seqalign_qu...
|
|
homology_line = Std.hsp_seqalign_homology_seq(Str(" ")+ Un...
|
|
subject_line = Std.hsp_seqalign_subject_name(Str("Sbjct"))+ Re...
|
|
blastn_hsp_header = score+ blastn_identical+ strand+ spaces_li...
|
|
blastp_hsp_header = score+ blastp_identical+ spaces_line
|
|
blastx_hsp_header = score+ blastp_identical+ frame+ spaces_line
|
|
tblastn_hsp_header = tblastn_score+ blastp_identical+ frame+ s...
|
|
tblastx_hsp_header = tblastn_score+ blastp_identical+ tblastx_...
|
|
alignment = Std.hsp_seqalign(query_line+ homology_line+ subjec...
|
|
hsp = Std.hsp(Group("hsp_header", NullOp())+ Rep(alignment))
|
|
hit = Std.hit(hit_descr+ hit_length+ Rep(Group("hsp", hsp)))
|
|
db_stats = Str(" Database:")+ ToEol()+ Str(" Posted date:"...
|
|
ungapped_lambda_stats = Str("Lambda K H")+ AnyEol()+(...
|
|
gapped_lambda_stats = Opt(Str("Gapped")+ AnyEol())+ Str("Lambd...
|
|
lambda_stats = ungapped_lambda_stats+ AnyEol()+ gapped_lambda_...
|
|
matrix_stats = SkipLinesUntil(Str("Matrix:"))+ _nv("Matrix: ",...
|
|
gap_penalties_stats = _nv("Gap Penalties: Existence: ", int_pa...
|
|
generic_info1 = _nv("Number of Hits to DB: ", int_stat("num_hi...
|
|
generic_info2 = _nv("length of query: ", int_stat("query_lengt...
|
|
hsp_info = _nv("Number of HSP's better than 10.0 without gappi...
|
|
frameshift_info = _nv("frameshift window, decay const: ", int_...
|
|
t_info = _nv("T: ", int_stat("t"))
|
|
a_info = _nv("A: ", int_stat("1"))
|
|
x1_info = _bit_info("X1: ", "x1")
|
|
x2_info = _bit_info("X2: ", "x2")
|
|
x3_info = _bit_info("X3: ", "x3")
|
|
s1_info = _bit_info("S1: ", "s1")
|
|
s2_info = _bit_info("S2: ", "s2")
|
|
blastn_ending = db_stats+ lambda_stats+ matrix_stats+ gap_pena...
|
|
blastp_ending = db_stats+ lambda_stats+ matrix_stats+ gap_pena...
|
|
blastx_ending = db_stats+ lambda_stats+ matrix_stats+ gap_pena...
|
|
tblastn_ending = db_stats+ lambda_stats+ matrix_stats+ gap_pen...
|
|
tblastx_ending = db_stats+ ungapped_lambda_stats+ matrix_stats...
|
|
format = Std.record(Group("appheader", NullOp())+ header+ Rep(...
|
|
blastn = replace_groups(format, (("appheader", blastn_appheade...
|
|
blastp = replace_groups(format, (("appheader", blastp_appheade...
|
|
blastx = replace_groups(format, (("appheader", blastx_appheade...
|
|
tblastn = replace_groups(format, (("appheader", tblastn_apphea...
|
|
tblastx = replace_groups(format, (("appheader", tblastx_apphea...
|
|
__warningregistry__ = { ( ' Bio.expressions was deprecated, as it ...
|